DoparParam-class: Enable parallel evaluation using registered dopar backend

In Bioconductor/BiocParallel: Bioconductor facilities for parallel evaluation

Enable parallel evaluation using registered dopar backend

Description

This class is used to dispatch parallel operations to the dopar backend registered with the foreach package.

Usage

DoparParam(stop.on.error=TRUE,
           RNGseed = NULL)

Arguments

stop.on.error

logical(1)

Stop all jobs as soon as one jobs fails (stop.on.error == TRUE) or wait for all jobs to terminate. Default is TRUE.

RNGseed

integer(1) Seed for random number generation. The seed is used to set a new, independent random number stream for each element of X. The ith element recieves the same stream seed, regardless of use of SerialParam(), SnowParam(), or MulticoreParam(), and regardless of worker or task number. When RNGseed = NULL, a random seed is used.

Details

DoparParam can be used for shared or non-shared memory computing depending on what backend is loaded. The doSNOW package supports non-shared memory, doParallel supports both shared and non-shared. When not specified, the default number of workers in DoparParam is determined by getDoParWorkers(). See the foreach package vignette for details using the different backends:

http://cran.r-project.org/web/packages/foreach/vignettes/foreach.pdf

DoparParam constructor

Return a proxy object that dispatches parallel evaluation to the registered foreach parallel backend.

There are no options to the constructor. All configuration should be done through the normal interface to the foreach parallel backends.

Methods

The following generics are implemented and perform as documented on the corresponding help page (e.g., ?bpisup): bpworkers, bpnworkers, bpstart, bpstop, bpisup, bpbackend, bpbackend<-, bpvec.

Author(s)

Martin Morgan mailto:[e-mail]

See Also

getClass("BiocParallelParam") for additional parameter classes.

register for registering parameter classes for use in parallel evaluation.

foreach-package for the parallel backend infrastructure used by this param class.

Examples

## Not run: 
# First register a parallel backend with foreach
library(doParallel)
registerDoParallel(2)

p <- DoparParam()
bplapply(1:10, sqrt, BPPARAM=p)
bpvec(1:10, sqrt, BPPARAM=p)

## set DoparParam() as the default for BiocParallel
## register(DoparParam(), default=TRUE)

## End(Not run)

Bioconductor/BiocParallel documentation built on Oct. 31, 2024, 6:58 a.m.